MolNFT v1 · #121590 · protein
Crystal structure of DR2231_E47A mutant in complex with dump and manganese
5HZZ: “Crystal structure of DR2231_E47A mutant in complex with dump and manganese”. X-ray diffraction, 2 ligands (UMP, MN), 7 pockets (best druggability 0.82). MolNFT v1 #121590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HZZ
- Type
- protein
- Length
- 559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DR2231
- UniProt
- Q9RS96
- Ligands
- UMP, MN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DR2231 | protein | 138 | 63% helix, 1% strand | Q9RS96 |
| B | DR2231 | protein | 139 | 63% helix, 1% strand | Q9RS96 |
| C, D | DR2231 | protein | 141 | 65% helix, 0% strand | Q9RS96 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.82 | 0.84 | 104 | UMP, MN |
| 2 | 88 | 0.41 | 0.78 | 18 | empty |
| 3 | 73 | 0.38 | 0.78 | 17 | empty |
| 4 | 78 | 0.38 | 0.77 | 19 | empty |
| 5 | 79 | 0.37 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3064 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 3022 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 223 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 126 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 123 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5HZZ · Crystal structure of DR2231_E47A mutant in complex with dUMP and manganese · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9RS96
- Elsewhere: RCSB PDB 5HZZ · PDBe 5HZZ · UniProt Q9RS96
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